Charges that Los Alamos National Laboratory scientist Wen Ho Lee passed US nuclear data to Beijing have roiled the national security establishment for months. They've caused Congress to approve a sweeping rejiggering of A-bomb development, and may force bureaucrats to reinspect 600 million pages of declassified material for inadvertent leakage of secrets.

The official who led the first probe into Lee's activities has resigned, and the whole affair is calling into question lawmaker assertions that China has penetrated the highest levels of US security and may be America's new cold-war adversary.

"If Lee is not charged, then we are really back to square one," says Jonathan Pollack, a Rand Corp. senior adviser for international policy.

The China spy case was explosive when made public this spring. A Senate report charged that the Los Alamos lab was at the center of an alleged Chinese espionage effort that dated back to the late 1970s and that unearthed secrets on every warhead in the US arsenal - including the most advanced, the W-88.

Lee was not named in the report. But leaks soon established him as a key suspect in the W-88 case. Perhaps the most damaging evidence against him was that investigators found classified nuclear testing codes on his unsecured home computer.

Lee was fired for this infraction, and espionage charges seemed imminent. Many lawmakers clamored to know why the Clinton administration hadn't moved faster on the Lee case.

Meanwhile, Congress voted to establish a new National Nuclear Security Administration within the Department of Energy to oversee weapons-related activities. It's not clear whether this will come to pass, as Energy Secretary Bill Richardson thinks it goes too far and is urging President Clinton to veto the legislation that contains the reorganization provision.

Other lawmakers decided that the administration was moving too fast to declassify millions of pages of secret material from the 1960s and '70s. A quick look turned up some key secrets that had been inadvertently made public - so Congress has ordered the administration to take another look at 600 million pages it has already stamped "cleared."

Then it turned out that a recent CIA director, John Deutch, had kept secret material on his unsecured home computer. In the atmosphere of the Lee case, the government had no choice but to strip Mr. Deutch of his security clearance.

"The national security part of the community in Washington has been utterly convulsed by [the Lee case] for over a year," says John Pike, a Federation for American Scientists intelligence expert.

But wait. If the respected former head of the CIA did some of the same things Lee did, does that mean...?

Oops. Never mind.

So far Lee has not been charged with espionage, and it now appears he never will be.

A recent bipartisan report by the Senate Committee on Governmental Affairs concluded that if nothing else, the Lee probe was hopelessly bungled. Investigators didn't bother to look at other suspects and fought over things such as whether to search Lee's computer.

"The story is one of investigatory missteps ... at all levels of government," said Sen. Fred Thompson (R) of Tennessee.

The Senate report noted circumstantial evidence such as the fact that Lee failed one polygraph test and his wife was eager to escort official Chinese visitors. But the report concluded that it is unclear whether the Chinese stole any nuclear secrets at all.

"We take no position ... whether W-88 or other nuclear-weapons information was in fact compromised," says the report.

China has some degree of knowledge about US weapons secrets, say experts. But the turmoil in the Lee case has thrown into question how much the Chinese really have, and where they got it.

"What precisely was the character of the information that China had acquired that attested to the role of espionage?" says Rand's Mr. Pollack. "There are other ways they could get this data that are not illegal."

Careful gleaning of declassified papers, for instance. Or, as Pollack points out, via the extensive high-technology transfers approved by successive US administrations since the early 1970s.

The Lee case became even murkier this week when the former chief of counterintelligence at Los Alamos, Robert Vrooman, charged that Lee was targeted because of his ethnicity, and that investigators did not bother to look at many other suspects who fit the same "suspicion matrix" criteria as Lee did.

Then the Energy Department intelligence investigator who pursued Lee in the first place, Notra Trulock, resigned on Tuesday. The reason, he said in a statement, is because he is being squeezed out of the China spy investigation - a charge the government has denied.